Single nucleotide polymorphism (SNP) identification and sequence analysis of 5′ flanking region of lactoferrin gene in Indian buffaloes (Bubalus bubalis)

Abstract: Lactoferrin, an iron (Fe3+) binding glycoprotein, found in a variety of body secretions of mammals, is a potential candidate gene in dairy cattle breeding for increasing resistance against infections especially in the mammary gland. The present study was undertaken with the objective of examining the 5′ flanking region of bubaline (Bubalus bubalis) lactoferrin gene to gain insight into the polymorphism existing in this region across different buffalo breeds. The 5′ flanking region of lactoferrin gene was analyzed by single strand conformation polymorphism (SSCP) in five different Indian buffalo breeds, viz. Murrah, Jaffarabadi, Marathwada, Toda and Pandharpuri. A total of 10 distinct SSCP patterns were observed which further revealed 13 polymorphisms with 8 transitions, 4 transversions and one deletion mutation upon sequence analysis. A total of 1056 bp 5′flanking region of bubaline lactoferrin gene was sequenced which was found to have 96% homology with Bos taurus, 91% with Capra hircus, 95%, Bos indicus, 92% with Ovis aries, 57% with Sus scrofa and 28% with Homo sapiens. From the polymorphisms identified in the 1056 bp 5′ flanking region, polymorphism at nucleotide position −209 was found to lie within a potential SP1 transcription factor binding site, while SNP at −19 was found in the vicinity of the TATA box. Two SNPs identified at −57 and −61 positions were found to be present in the vicinity of putative estrogen response element. Another SNP at −636 position was found to be present in the vicinity of putative recognition sequence for IRF-1 which serves as a transcriptional activator for interferon genes and interferon inducible genes. The SNPs identified in the lactoferrin promoter region may serve as potential candidate genetic marker(s) in buffaloes for disease resistant traits. [Copyright &y& Elsevier]